HGNC NewsLetter, Summer 2023

Some of you will be interested in this Summer 2023 HUGO Gene Nomenclature Committee (HGNC) NewsLetter. As you may be aware, these update issues come out four times a year.

Summer newsletter 2023

HGNC, VGNC, Newsletters · August 2023

HGNC is on the move…

Later in the year, the HGNC team will be moving from our current office within EMBL-EBI in Hinxton to the University of Cambridge Haematology Department on the Cambridge Biomedical Campus. Several members of the HGNC team are already employees of Cambridge University; those that are currently employed by EMBL-EBI will initially be granted visitor status and will transition to being employed by the university in due course. The HGNC and VGNC compute will remain at EMBL-EBI, meaning that our website users will not notice any change and the project will continue to be a collaboration between Cambridge University and EMBL-EBI. Watch this space for photos of our new office in future newsletters!
Update on genes with the ‘stable’ tag

We now have 3262 approved gene symbols marked with our stable tag, meaning we regard these symbols to be unlikely to change in future. Genes that have recently had this tag added include the protein-coding genes: ABRAXAS1 (abraxas 1, BRCA1 A complex subunit); FA2H (fatty acid 2-hydroxylase); HAAO (3-hydroxyanthranilate 3,4-dioxygenase); HNMT (histamine N-methyltransferase); HNRNPA0 (heterogeneous nuclear ribonucleoprotein A0); MLPH (melanophilin); PRODH and the non-coding RNA gene RMRP (RNA component of mitochondrial RNA processing endoribonuclease).

Out of the 141 genes that have had the stable tag added over the last three months, just 7 of these genes had their gene name changed as part of the pre-stabilisation review process. The names of BNC1 and BNC2 were updated from “basonuclin 1” and “basonuclin 2” to the more informative “basonuclin zinc finger protein 1” and “basonuclin zinc finger protein 2”; SHOX and SHOX2 were updated to replace potentially pejorative “short stature homeobox” with the more neutral “SHOX homeobox”; TUBGCP2, TUBGCP4 and TUBGCP6 were updated to replace “tubulin gamma complex associated protein” with “tubulin gamma complex component” to reflect more recent functional data on the encoded proteins. No gene symbols were changed.
Updates to placeholder symbols

The symbol and name of C4orf48 was updated to NICOL1 for “NELL2 interacting cell ontogeny regulator 1” after fruitful discussions with groups working on this gene. A 2023 Nature Communications paper published the symbol “NICOL” for “NELL2-interacting cofactor for lumicrine signalling”; the addition of the 1 makes a unique symbol for searching and the term “cofactor for lumicrine signalling” has been replaced with “cell ontogeny regulator” to reflect the wider function of the protein encoded by this gene.

The nomenclature of the FAM104 family was updated from FAM104A and FAM104B to VCF1, “VCP nuclear cofactor family member 1” and VCF2, “VCP nuclear cofactor family member 2”. The symbol VCF1 was used in a recent preprint with the name “VCP/p97 Cofactor FAM104 1”. We explained to the researchers that there is no need to reference FAM104 in the new gene names, as FAM104A is recorded as a previous symbol and is therefore still fully searchable. After discussions with two groups, the symbols VCF1 and VCF2 were agreed upon for both paralogs, along with the approved names “VCP nuclear cofactor family members 1 and 2”.
New gene groups

We continue to add new gene groups, with recent additions of the following families:

Thrombospondin family
Isthmin family
Methionine adenosyltransferase family

Gene Symbols in the News

In virus-related news, the gene product of BTN3A3 has been shown to provide defence against most avian influenza viruses by blocking viral replication in the nose, throat and lungs. All pandemic-causing viruses thus far studied, and most human viruses, are resistant to BTN3A3 — so, this may provide a predictor for which zoonotic viruses are more likely to possess future potential to cross over into humans.

In COVID news, people carrying two copies of the HLA-B variant known as HLA-B15:01 are more than eight times more likely than the average person to experience asymptomatic COVID-19. This protection appears to be independent of other risk factors for COVID-19 severity. A different study has found an association between a SNP near to the FOXP4 locus and the probability that an individual will develop long COVID. The FOXP4 gene is expressed in the lung and in immune-related cells.

A study that recruited people between the ages of 20 and 40 and subjected them to the “Cooper 12-minute run test” over the course of eight weeks has shown that a number of SNPs, including one at the ACTN3 gene, are associated with increased cardiorespiratory fitness as a result of endurance training.

GDNF gene therapy, already in trial for treating Parkinson disease, could one day be used to treat severe alcohol addiction. A study of macaques found that treating individuals who were addicted to alcohol with macaque GDNF resulted in increased dopamine expression and a reduction in the decision of these monkeys to consume alcohol by up to 90%. Due to the need for brain surgery, GDNF gene therapy would only be plausible for the most severe human cases, if it were ever approved for this usage.

In further animal gene therapy news, feral female cats can be effectively sterilised by a single injection of the AMH gene into a muscle. The muscle then produces the AMH hormone at high levels, far higher than that naturally produced by feline ovaries. This treatment would prevent the need to perform stressful and expensive spaying operations on feral populations.

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